Horticultural plant material offers several advantages for isolating exosomes and other natural plant-derived exosome-like nanoparticles (PDENs) due to the accessibility and affordability of plant material for widespread applications. This study aims to explore the impacts of the tomato genotype (‘Admiro’, ‘Roma’, ‘Brooklyn’, ‘Marmande’ and ‘Betalux’) and the main cultivation parameters in controlled environment agriculture on the yield and properties of their PDENs for pharmaceutical and cosmeceutical applications. The PDEN yield, size distribution, and antioxidative properties of young tomato seedlings were evaluated. The ‘Betalux’ tomato was distinguished by a remarkably higher nanoparticle concentration and a uniform size distribution and was selected for further experiments. The impact of cultivation temperature (18, 22, and 26 °C), nitrogen nutrition (0, 250, and 500 mg L−1), and the lighting photosynthetic photon flux density (PPFD; 150, 250, and 450 µmol m−2 s−1) on nanoparticle properties was investigated. Optimal conditions consisting of a temperature of 22 °C, 250 mg L−1 nitrogen nutrition, and 250 µmol m−2 s−1 lighting PPFD were used as a reference. Optimal temperature, nitrogen nutrition, and lighting intensity resulted in the highest nanoparticle yield, the most uniform particle distribution, and the highest impact of PDEN preparations on keratinocyte metabolic activity. Deviation from optimal cultivation conditions reduced the tomato biomass and the PDEN protein and yield.